Juvenile Steelhead and Stream Habitat Conditions Steelhead and Coho Salmon Life History Prepared by: DW ALLEY & Associates, Fishery Consultant

Size: px

Start display at page:

Download "Juvenile Steelhead and Stream Habitat Conditions Steelhead and Coho Salmon Life History Prepared by: DW ALLEY & Associates, Fishery Consultant"

Lawrence Holland
5 years ago
Views:

1 Juvenile Steelhead and Stream Habitat Conditions Steelhead and Coho Salmon Life History Prepared by: DW ALLEY & Associates, Fishery Consultant I-1. Steelhead and Coho Salmon Ecology Migration. Adult steelhead in small coastal streams typically migrate upstream from the ocean through an open sandbar after several prolonged storms; the migration seldom begins earlier than December and may extend into May if late spring storms develop. Many of the earliest migrants tend to be smaller than those entering the stream later in the season. Adult fish may be blocked in their upstream migration by barriers such as bedrock falls, wide and shallow riffles and occasionally logjams. Man-made objects, such as culverts, bridge abutments and dams are often significant barriers. Some barriers may completely block upstream migration, but many barriers in coastal streams are passable at higher streamflows. If the barrier is not absolute, some adult steelhead are usually able to pass in most years, since they can time their upstream movements to match optimal stormflow conditions. We located partial migrational barriers in the San Lorenzo River Gorge caused by a wide riffle that developed below a bend in 1998 (Rincon riffle) and a large boulder field discovered in 1992 that created a falls (above Four Rock). Both of these impediments were probably passable at flows above approximately cubic feet per second (cfs) as they were observed in 2002, though no data were collected to confirm this. A split channel had developed at the Rincon riffle by 2002 and in 2007 there existed a steep cascade where the channels rejoined, making adult steelhead passage up the main channel difficult. In 2008, the steep cascade was gone, offering much easier fish passage up the main channel. The boulder field at Four Rock was partially modified in 2008, though we have not examined the results. The steep cascade reappeared at the end of the Rincon riffle by In most years these are not passage problems. However, in drought years and years when storms are delayed, they can be serious barriers to steelhead and especially coho salmon spawning migration. In the West Branch of Soquel Creek, there are Girl Scout Falls I and II that impede adult passage. Based on juvenile sampling, adult steelhead pass Girl Scout Falls I in most years but seldom pass Girl Scout Falls II. Coho salmon often have more severe migrational challenges because their migration period, November through early February, is often prior to the stormflows needed to pass shallow riffles, boulder falls and partial logjam barriers. Access is also a greater problem for coho salmon because they die at maturity and cannot wait in the ocean an extra year if access is poor due to failure of sandbar breaching during drought or delayed stormflow. In recent years until 2008, the rainfall pattern has generally brought early winter storms to allow for good coho access to the San Lorenzo system, though only a small number of apparent strays have been detected at the Felton fish ladder and trap. Smolts (young steelhead and coho salmon which have physiologically transformed in preparation for ocean life) in local coastal streams tend to migrate downstream to the lagoon and ocean in March through early June. In streams with lagoons, young-of-the-year (YOY) and yearling fish

2 may spend several months in this highly productive lagoon habitat and grow rapidly. In some small coastal streams, downstream migration can occasionally be blocked or restricted by low flows due primarily to heavy streambed percolation or early season stream diversions. Flashboard dams or sandbar closure of the stream mouth or lagoon are additional factors that adversely affect downstream migration. However, for most local streams, downstream migration is not a major problem except under drought conditions. Spawning. Steelhead and coho salmon require spawning sites with gravels (from 1/4" to 3 1/2" diameter) having a minimum of fine material (sand and silt) and with good flows of clean water moving over and through them. Flow of oxygenated water through the redd (nest) to the fertilized eggs is restricted by increased fine materials from sedimentation and cementing of the gravels with fine materials. Flushing of metabolic wastes is also hindered. These restrictions reduce hatching success. In many local streams, steelhead appear to successfully utilize spawning substrates with high percentages of coarse sand, which probably reduces hatching success. Steelhead spawning success may be limited by scour from winter storms in some Santa Cruz County streams. Steelhead that spawn earlier in the winter are more likely to have their redds washed out or buried by the greater number of winter and spring storms that will follow. However, unless hatching success has been severely reduced, survival of eggs and alevins is usually sufficient to saturate the limited available rearing habitat in most small coastal streams and San Lorenzo tributaries. However, in the mainstem San Lorenzo River downstream of the Boulder Creek confluence, spawning success in the river may be an important limiting factor. YOY fish production is related to spawning success, which is a function of the spawning habitat quality, the pattern of storm events and ease of spawning access to upper reaches of tributaries, where spawning conditions are generally better. Rearing Habitat. In the mainstem San Lorenzo River, downstream of the Boulder Creek confluence, many steelhead require only one summer of residence before reaching smolt size. This is also the case in the Soquel Creek mainstem and lagoon. Except in streams with high summer baseflows (greater than about 0.2 to 0.4 cubic feet per second (cfs) per foot of stream width), steelhead require two summers of residence before reaching smolt size. This is the case for most juveniles inhabiting San Lorenzo River tributaries and the mainstem upstream of the Boulder Creek confluence. This is also the case for most juveniles in the East and West Branches of Soquel Creek, the Aptos watershed (except its lagoon) and the Corralitos sub-watershed except in wetter years such as Juvenile steelhead are generally identified as YOY (first year) and yearlings (second year). The slow growth and often two-year residence time of most local juvenile steelhead indicate that the year class can be adversely affected by low streamflows or other problems (including overwintering survival) during either of the two years of residence. Nearly all coho salmon, however, smolt after one year under most conditions, despite their smaller size. Growth of YOY steelhead and coho salmon appears to be regulated by available insect food (determined by substrate conditions in fastwater habitat and insect drift rate), although escape cover (hiding areas, provided by undercut banks, large rocks which are not buried or "embedded" in finer

3 substrate, surface turbulence, etc.) and water depth in pools, runs and riffles are also important in regulating juvenile numbers, especially for larger fish. Densities of yearling and smolt-sized steelhead in small streams, the upper San Lorenzo (upstream of the Boulder Creek confluence) and San Lorenzo tributaries, are usually regulated by water depth and the amount of escape cover during low-flow periods (July October) and by over-winter survival in deep and/or complex pools. In most small coastal streams, availability of this "maintenance habitat" provided by depth and cover appears to determine the number of smolts produced (Alley 2006a; 2006b; 2007; Smith 1982). Abundance of food (aquatic insects and terrestrial insects that fall into the stream) and fastwater feeding positions for capture of drifting insects in "growth habitat" (provided mostly in spring and early summer) determine the size of these smolts. Study of steelhead growth in Soquel Creek has noted that growth is higher in winter-spring compared to summer-fall (Sogard et al. 2009). It was determined that in portions of a watershed that are capable of growing YOY juvenile steelhead to smolt size their first growing season (Size Class II =>75 mm Standard Length in fall), the density of YOY that obtain this size was positively associated with the mean monthly streamflow for May September (Alley et al. 2004). Furthermore, it has been shown that the density of slower growing YOY in tributaries was positively associated with the annual minimum annual streamflow (Alley et al. 2004). Aquatic insect production is maximized in unshaded, high gradient riffles dominated by relatively unembedded substrate larger than about 4 inches in diameter. Growth of yearling steelhead shows a large increase during the period of March through June. Larger steelhead then may smolt as yearlings. For steelhead that stay a second summer, mid to late summer growth is very slight in many tributaries (or even negative in terms of weight) as reduced flow eliminates fastwater feeding areas and reduces insect production and drift. A short growth period may occur in fall and early winter after leaf drop from riparian trees, after increased streamflow from early storms, and before water temperatures decline below about 48ºF or water clarity becomes too turbid for feeding. The "growth habitat" provided by higher flows in spring and fall (or in summer for the mainstem San Lorenzo River) is very important, since ocean survival to adulthood increases exponentially with smolt size. During summer in the mainstem San Lorenzo River, downstream of the Boulder Creek confluence, steelhead use primarily fastwater habitat where insect drift is greatest. This habitat is found in deeper riffles, heads of pools and faster runs. YOY and small yearling steelhead that have moved down from tributaries can grow very fast in this habitat if streamflows are high and sustained throughout the summer. The shallow riffle habitat in the upper mainstem is used almost exclusively by small YOY, although most YOY are in pools. In the warm mainstem Soquel Creek, downstream of Moores Gulch, juvenile steelhead use primarily heads of pools in all but the highest flow years, with some YOY using shallower runs and riffles. In the Soquel mainstem, upstream of Moores Gulch, and in the two branches (East and West), juvenile steelhead use primarily pool habitat and deeper step-runs where cover is available. Riffles are used primarily by small YOY in the upper mainstem more so than in the branches, where they are shallower.

4 In summer in San Lorenzo tributaries, the upper San Lorenzo mainstem above the Boulder Creek confluence, in the Aptos watershed and in the Corralitos sub-watershed, the primary habitat for soon-to-smolt steelhead and smaller YOY is pools and step-runs because riffles and runs are very shallow. Riffle and run habitat offers limited escape cover. Primary feeding habitat is at the heads of pools and in deeper pocket water of step-runs. The deeper the pools, the more value they have. Higher streamflow enhances food availability, surface turbulence (as overhead cover) and habitat depth, all factors that increase steelhead densities and growth rates. Where found together, young steelhead use pools and fastwater in riffles and runs/step-runs, while coho salmon use primarily pools, being poorer swimmers. Juvenile steelhead captured during fall sampling included a smaller size class of juveniles less than (<) 75 mm (3 inches) Standard Length (SL); these fish would almost always require another growing season before smolting. The larger size class included juveniles 75 mm SL or greater (=>) and constituted fish that are called "soon-to-smolt size" because a majority will likely out-migrate the following spring and because fish smaller than this very rarely smolt the following spring. Smolt size was based on scale analysis of out-migrant smolts captured in in the lower San Lorenzo River. This size class in fall may include fast growing YOY steelhead inhabiting the mainstems of the San Lorenzo River and Soquel Creek, lower reaches of larger San Lorenzo tributaries, and lower reaches of Corralitos and Aptos creeks. It also includes slower growing yearlings and older fish inhabiting all watershed reaches. The lower San Lorenzo mainstem below Zayante Creek typically has sufficient baseflow every year to grow a high proportion of YOY to smolt size in one year, as does lower Soquel Creek below Moores Gulch. In these lower reaches with high growth potential, factors that determine YOY densities are important in determining soon-to-smolt densities, such as number of adult spawners, spawning success and/or recruitment of YOY from nearby tributaries. There is a group of sites with intermediate YOY growth potential which may produce a higher proportion of YOY that reach potential smolt size by fall in addition to yearlings if streamflow is high and/or YOY densities are low. These reaches include the middle mainstem San Lorenzo between Boulder and Zayante creek confluences, upper Soquel mainstem above the Moores Gulch confluence, lower East Branch Soquel, Aptos Creek mainstem and lower Corralitos below Rider Creek confluence. In above average baseflow years, these reaches are relatively productive for soon-to-smolt-sized YOY unless large, late stormflows reduce YOY survival or insufficient adults spawn after the late storms to saturate habitat with YOY. A basic assumption in relating juvenile densities to habitat conditions where they are captured is that juveniles do not move substantially from where they are captured during the growing season. This assumption is reasonable because at sites in close proximity, such as adjacent larger

5 mainstem and smaller tributary sites, there are consistent differences in fish size, such as juveniles that are consistently larger in the mainstem sites where streamflow is greater and there is more food (D. Alley pers. observation). In other cases, there are differences in fish size between sunny productive habitats and shady habitats where food is scarce. This indicates a lack of movement between sites. In addition, Davis (1995), during a study of growth rates in various habitat types, marked juvenile steelhead in June in Waddell Creek and recaptured the same fish in September in the same (or immediately adjacent) habitats where they had been marked. During the Sogard et al. (2009) work, many juveniles that had been PIT tagged early in the growing season were recaptured in the same habitats later in the fall, and we detected very few of their marked fish in other downstream sites through the years of tagging, with most being captured in close proximity of where they were originally tagged. Evidence is lacking that would indicate ecologically significant juvenile movement upstream during the dry season, and the concern that summer flashboard dams without ladders may impede upstream movements of juvenile salmonids appears unfounded. Shapovalov and Taft (1954), after 9 consecutive years of fish trapping on Waddell Creek, detected very limited upstream juvenile steelhead movements; most of the relatively limited movement occurred in winter. Overwintering Habitat. Shelter for fish against high winter flows is provided by deeper pools, undercut banks, side channels, large unembedded rocks and large wood clusters. Over-wintering survival is usually a major limiting factor, since yearling fish are usually less than 10-20% as abundant as YOY. In winters with significant stormflows (i.e. 1982, 1995, 1998 and 2006), overwintering habitat may be the most critical for steelhead production. In the majority of years when bankfull or greater stormflows occur, these refuges are critical, and it is unknown how much refuge is needed. The remaining coho streams, such as Gazos, Waddell and Scott creeks, have considerably more instream wood than others (Leicester 2005).

2011 SUMMARY REPORT Juvenile Steelhead Densities in the San Lorenzo, Soquel, Aptos and Corralitos Watersheds, Santa Cruz County, CA

2011 SUMMARY REPORT Juvenile Steelhead Densities in the San Lorenzo, Soquel, Aptos and Corralitos Watersheds, Santa Cruz County, CA 211 SUMMARY REPORT Juvenile Steelhead Densities in the San Lorenzo, Soquel, Aptos and Corralitos Watersheds, Santa Cruz County, CA, Aquatic Biology Don Alley, Jerry Smith and Chad Steiner, Fishery Biologists